Stupidity: The Analyst wishes to hide the true identity of Neo from anyone inside the Matrix, so his appearance is altered. But in this new Matrix Neo is also named Thomas Anderson, his name from before he was pulled from the Matrix originally, and he is a famous game developer that created a video game series called "The Matrix." It is frankly astounding that anyone actively looking for Thomas Anderson would not immediately see through this ruse and instead would be fooled by balding hair.
Stupidity: Lyla does not like the idea of Mickey fighting and initially does not want him to agree to the fight. Lyla eventually tells him "okay", but he must stop when she tells him to stop. This may give her a reason to go to Dubai, UAE with him, but she is about 8 months pregnant. An international flight has some risks plus she would be far away from her OB-GYN doctor if there were a complication. She should have had enough sense to avoid international flights/traveling so close to her due date.
Stupidity: Patrick told Dwayne to get Cisneros to kill Zara, apparently because he believed Cisneros could get the job done. Cisneros went into Zara's house with his gun ready to shoot, but not before pinpointing Zara's location. He saw the refrigerator door open yet entered the room without looking left and right (behind the door); Zara was able to disarm him. Zara was also able to escape Cisneros' repeated crazy swings at her with a samurai sword. Zara fatally "sliced" his neck with a pizza cutter. (00:21:44 - 00:23:07)
Stupidity: Right before the movie's final battle, Sub-Zero taunts Cole with his wife's necklace and makes him chase him into a portal. Sonya was right next to Cole, and she did not come along with him. They had previously planned to take on Sub-Zero together, but apparently she just left him to chase Sub-Zero alone to an unknown location.